lamindb 0.45a1__py3-none-any.whl → 0.46a1__py3-none-any.whl

lamindb/dev/storage/{_file.py → file.py}

@@ -6,11 +6,11 @@ from typing import Union
 import anndata as ad
 import fsspec
 import pandas as pd
+from lamin_logger import logger
 from lamindb_setup import settings
+from lamindb_setup.dev import StorageSettings
 from lamindb_setup.dev.upath import UPath, infer_filesystem
-from lnschema_core.models import File
-
-from lamindb._file_access import attempt_accessing_path
+from lnschema_core.models import File, Storage
 
 try:
     from ._zarr import read_adata_zarr
@@ -20,6 +20,51 @@ except ImportError:
         raise ImportError("Please install zarr: pip install zarr")
 
 
+AUTO_KEY_PREFIX = ".lamindb/"
+
+
+# add type annotations back asap when re-organizing the module
+def auto_storage_key_from_file(file: File):
+    if file.key is None:
+        return f"{AUTO_KEY_PREFIX}{file.id}{file.suffix}"
+    else:
+        return file.key
+
+
+def attempt_accessing_path(file: File, storage_key: str):
+    if file.storage_id == settings.storage.id:
+        path = settings.storage.key_to_filepath(storage_key)
+    else:
+        logger.warning(
+            "file.path() is slower for files outside the currently configured storage"
+            " location"
+        )
+        storage = Storage.select(id=file.storage_id).one()
+        # find a better way than passing None to instance_settings in the future!
+        storage_settings = StorageSettings(storage.root, instance_settings=None)
+        path = storage_settings.key_to_filepath(storage_key)
+    # the following is for backward compat
+    if storage_key.startswith(AUTO_KEY_PREFIX) and not path.exists():
+        logger.warning(
+            "You have auto-keyed files in your storage root, please move them into"
+            f" {AUTO_KEY_PREFIX} within your storage location"
+        )
+        # try legacy_storage_key in root
+        for previous_prefix in ["", "lndb/"]:
+            legacy_storage_key = storage_key.replace(AUTO_KEY_PREFIX, previous_prefix)
+            path = settings.storage.key_to_filepath(legacy_storage_key)
+            if path.exists():
+                return path
+    return path
+
+
+# add type annotations back asap when re-organizing the module
+def filepath_from_file(file: File):
+    storage_key = auto_storage_key_from_file(file)
+    path = attempt_accessing_path(file, storage_key)
+    return path
+
+
 def read_adata_h5ad(filepath, **kwargs) -> ad.AnnData:
     fs, filepath = infer_filesystem(filepath)
 

lamindb/dev/storage/{_object.py → object.py}

@@ -9,6 +9,7 @@ def infer_suffix(dmem, adata_format: Optional[str] = None):
     """Infer LaminDB storage file suffix from a data object."""
     if isinstance(dmem, AnnData):
         if adata_format is not None:
+            # below should be zrad, not zarr
             if adata_format not in ("h5ad", "zarr"):
                 raise ValueError
             return "." + adata_format

lamindb/dev/utils.py

@@ -0,0 +1,9 @@
+def attach_func_to_class_method(func_name, cls, globals):
+    implementation = globals[func_name]
+    target = getattr(cls, func_name)
+    # assigning the original class definition docstring
+    # to the implementation only has an effect for regular methods
+    # not for class methods
+    # this is why we need @doc_args for class methods
+    implementation.__doc__ = target.__doc__
+    setattr(cls, func_name, implementation)

lamindb/types.py

@@ -5,6 +5,14 @@
 
    PathLike
    DataLike
+   StrField
+   ListLike
    TransformType
 """
-from lnschema_core.types import DataLike, PathLike, TransformType  # noqa
+from lnschema_core.types import (  # noqa
+    DataLike,
+    ListLike,
+    PathLike,
+    StrField,
+    TransformType,
+)

{lamindb-0.45a1.dist-info → lamindb-0.46a1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.45a1
+Version: 0.46a1
 Summary: LaminDB: Manage R&D data & analyses.
 Author-email: Lamin Labs <laminlabs@gmail.com>
 Requires-Python: >=3.8
@@ -8,9 +8,9 @@ Description-Content-Type: text/markdown
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
-Requires-Dist: lnschema_core==0.36.1
-Requires-Dist: lamindb_setup==0.47.11
-Requires-Dist: lamin_logger==0.7.1
+Requires-Dist: lnschema_core==0.38.0
+Requires-Dist: lamindb_setup==0.48.1
+Requires-Dist: lamin_logger==0.7.4
 Requires-Dist: erdiagram>=0.1.2
 Requires-Dist: rapidfuzz
 Requires-Dist: pydantic[dotenv]
@@ -24,7 +24,7 @@ Requires-Dist: pandas
 Requires-Dist: botocore==1.29.76 ; extra == "aws"
 Requires-Dist: boto3==1.26.76 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.5.0 ; extra == "aws"
-Requires-Dist: lnschema_bionty==0.24.0 ; extra == "bionty"
+Requires-Dist: lnschema_bionty==0.25.5 ; extra == "bionty"
 Requires-Dist: readfcs>=1.1.3 ; extra == "fcs"
 Requires-Dist: fsspec[gs]==2023.5.0 ; extra == "gcp"
 Requires-Dist: nbproject>=0.9.0 ; extra == "jupyter"
@@ -57,7 +57,9 @@ Provides-Extra: zarr
 
 # LaminDB
 
-Open-source data lake to manage your existing data in your existing infrastructure.
+Open-source data lake, warehouse & feature store for biology.
+
+Manage your existing data & analyses in your existing infrastructure.
 
 ```{warning}
 
@@ -69,21 +71,22 @@ Update 2023-06-14:
 - The last version before the migration is 0.41.2.
 ```
 
-## Features
+## What?
 
-Free:
+LaminDB is a free & open-source Python library allowing you to:
 
-- Track [data lineage](https://lamin.ai/docs/guide/data-lineage) across notebooks, pipelines & apps.
-- Manage [biological registries, ontologies & features](https://lamin.ai/docs/biology/registries).
-- [Query, search & look up anything](https://lamin.ai/docs/guide/select), [manage & migrate custom schemas](https://lamin.ai/docs/setup/migrate).
-- [Persist, load](https://lamin.ai/docs/guide/files-records#in-memory-objects) & [stream data objects](https://lamin.ai/docs/guide/stream) with a single line of code.
-- [Idempotent](https://lamin.ai/docs/faq/idempotency) and [ACID](https://lamin.ai/docs/faq/acid) operations.
-- Use a mesh of LaminDB instances and [share them in a hub](https://lamin.ai/laminlabs) akin to GitHub.
+- Manage files & datasets while tracking [provenance](https://lamin.ai/docs/guide/data-lineage) across pipelines, notebooks & apps.
+- Manage biological [registries](https://lamin.ai/docs/biology/registries), [ontologies](https://lamin.ai/docs/bionty/) & features.
+- Rely on integrity & quality through largely automated data validation and [idempotent](https://lamin.ai/docs/faq/idempotency) & [ACID](https://lamin.ai/docs/faq/acid) operations.
+- Use a simple API for common tasks like:
+  - [Queries, searches & look ups](https://lamin.ai/docs/guide/select).
+  - Saving, loading & [streaming](https://lamin.ai/docs/guide/stream) of data objects.
+- Collaborate across a mesh of LaminDB instances ([share them in a hub](https://lamin.ai/laminlabs) akin to GitHub).
 
-Enterprise:
+You can combine LaminDB with LaminApp & consulting services on an enterprise plan:
 
-- Explore, share data & submit samples with LaminApp (deployable in your infrastructure).
-- Receive support, code templates & services for a BioTech data & analytics platform.
+- LaminApp: Explore & collaborate on data in a UI (deployable in your infrastructure).
+- Services: Support & code templates for a BioTech data & analytics platform.
 
 ## Usage overview
 

lamindb-0.46a1.dist-info/RECORD

@@ -0,0 +1,36 @@
+lamindb/__init__.py,sha256=oNhOp57mSmXcWLsgnviLZJE52YLsoWR0x0wdB0TvZKA,2843
+lamindb/_context.py,sha256=HxFGplpi4KP5X4pQ0WOhN85rEv3J0GSNVPWtx4EPlPQ,14229
+lamindb/_dataset.py,sha256=Bu5Peo7KS4V6mRWuaWTtQwshtPRKW13JbnvsHXY_c58,5322
+lamindb/_delete.py,sha256=wQqi17_YOO1QT-eKgHycewrw_qpbsRLv7siBkhynyUk,1245
+lamindb/_feature_set.py,sha256=eUzfPYY2zRhiN9KSNgqJaryM1RRFH_n_EXN1Bri5tb4,4896
+lamindb/_file.py,sha256=AR4EVjHnF-vnGxC_101ms1DGbK8NEwHeLNue0S14FFg,24407
+lamindb/_from_values.py,sha256=vbxTujbmmX6zSTBhOwrt6k-VGgA-QGAtjvYbzqEHNnw,8188
+lamindb/_logger.py,sha256=d1jQdFL4gMKbzcc1dMOgKoEaUlWhyK-VsnxYLlG9caY,48
+lamindb/_orm.py,sha256=1T-KpGJW8lVjsyzX7u3OTV1SsFqE0jDoSnPXK4kGO38,12216
+lamindb/_save.py,sha256=gQvioV_ZEw_R6vcLJIiqRcr21vb_0ivJqzwCmj4bPFI,7495
+lamindb/_select.py,sha256=lh1nPb0UUYYQCiHQeeZ6J8xfSufQYxYmmmdIKYZKZ4I,763
+lamindb/_transform.py,sha256=EG87wlUffGI_-N92Qu-qklNRs4hTEeHpEtspYIVGKtc,911
+lamindb/_view.py,sha256=TuWkdIFu8H__5PJK-L1m9CRySmyRPCgcAxZpue8Q154,1455
+lamindb/types.py,sha256=svg5S_aynuGfbEOsbmqkR_gF9d9YMzfOkcvGN37Rzvg,232
+lamindb/dev/__init__.py,sha256=HvTL5KH73egC4_zFmhxw_OA1Wyzx4phP7L1HvaR6xKw,268
+lamindb/dev/_settings.py,sha256=1UXCQF1fwYQoqZ3FKb5v5-xaJbggrkgeddIVU5iMDhY,2526
+lamindb/dev/hashing.py,sha256=ZPdGg7w-hyzJqQcxqHiVV5TF3x2CqNBZHrc5KVi4vFU,943
+lamindb/dev/utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
+lamindb/dev/datasets/__init__.py,sha256=4HzUArEtxe_QXMCiqmSFXhurCU09iKRWfUL0wLXbWpQ,905
+lamindb/dev/datasets/_core.py,sha256=kSki3AXiefI05XwmbR8eqlx1-5anTwKluWjDOXYpuXM,9792
+lamindb/dev/datasets/_fake.py,sha256=S8mNho-oSh1M9x9oOSsUBLLHmBAegsOLlFk6LnF81EA,942
+lamindb/dev/storage/__init__.py,sha256=ux4W0cpr5jRn5bLjawMqVK4GIwTgp7eKSf_lgdo3lBk,463
+lamindb/dev/storage/_anndata_sizes.py,sha256=OOM9mJmhvho5JacsuMsHTXoWfvF0vjxRvg_Pi9VkAo4,730
+lamindb/dev/storage/_backed_access.py,sha256=kTUKeC7QNSC_sJi2ZHwMV5FJFe4aH-P7oJAcR4NN-HY,15505
+lamindb/dev/storage/_zarr.py,sha256=7W1Jos1QOOF3f41uML_arQoDTNPZVpRyP2m3SLWaCAo,2766
+lamindb/dev/storage/file.py,sha256=RzKvbyiqSwvYbbLNs5C4zsXXnQP8L24PSyCEDWmacn0,5911
+lamindb/dev/storage/object.py,sha256=x8sy23WqkGir2sg2c3AngQPgv0RbErEA6cpvVN0Zc4I,945
+lamindb/schema/__init__.py,sha256=PznznlFvbeNSZKpn1RS6Gv0JMXFkLmU2_ej_1hVLSTs,796
+lamindb/schema/_core.py,sha256=nWR3X_rNd1AbWw3naMiBi8ppAEpqIDyEYqM54feRB_s,766
+lamindb/setup/__init__.py,sha256=8-0F2C4Glx23-b8-D_1CBGgRBM5PppVhazhoXZYOLsg,275
+lamindb/setup/dev/__init__.py,sha256=iD0f2lx_Hgp-udkiPGal7si5waJSOgvnG6Id-g1mMOY,213
+lamindb-0.46a1.dist-info/entry_points.txt,sha256=MioM8vSpKwXxY3geNBwjo1wnwy1l15WjJYlI3lpKuZI,53
+lamindb-0.46a1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.46a1.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.46a1.dist-info/METADATA,sha256=i9kIaqmFJPiFBuHX9QI2_z-Se6FYtoqSZdC_-9LF0TE,11035
+lamindb-0.46a1.dist-info/RECORD,,